I am having the same problem, I'm running 2.00.06 on Windows 7 Service Pack 1 but in windows vista service pack 2 compatibility (without compatibility or in any other compatibility mode the game CTDs either straight away or after a few minutes in) , it is my only version, so it has nothing to do with older versions. It seems to happen to me when I save after sighting a Naval base, regardless if I save on the planet or if I leave the planet and save. Coincidentally when I do sight Naval Bases some of the craft that are supposed to be on board the ships seemed to have slipped out of the ships and are floating and emitting an SOS, which obviously is not supposed to happen. It has happened so far on Earth when I went looking for the underwater base which wasn't there anyway. Just found underwater jump portals, no bases under the ships, and most recently on the planet where New America Ter/Ins Star Station is. I went down to the planet to drop off some mining drones near the SBase, flew over to the 2 NBases to have a look, left the planet, saved and then when I tried to restore the savegame it CTD while loading, with the message -Save file corrupt invalid dynamic end marker- I did try a few times with the same result. Thankfully I saved earlier in a different slot so I don't have to restart the Roam. But I'd rather this not keep happening every time I fly over a Naval Base, which I suspect is the cause because when I saved on Earth in Nbase 331 without sighting the ships there was no problem restoring the save game, only after I sighted them and saved it happened.
By the way I'm also doing the ACM A World Apart on a different save, I'm supposed to send a wing of fighters from the firebase to recon an enemy base and I have no idea what command to send them under or how to send them there considering I can't use a waypoint marker to designate where they need to recon, I assume it has something to do with designating a target with Cntrl P then using Fleet C&C to apply the order but what do I target at which enemy base and under what order, SAD, SEAD, Patrol, the manual is not clear on which one is used for a Recon mission and the mission instruction doesn't specify which base, My guess is the one in the NE, but an earlier instruction said not to go near there under any circumstance, and to paint a target I might as well just go there myself and recon it, so I'm a little confused. And please, no flak, this game is already giving me a hell of a hard time, just a solution and a bit of straight forward guidance would be appreciated.